In 1932 he entered flight training school at the Naval Air Station Pensacola, Florida; after graduating as a naval aviator in 1933 he served as navigator and executive officer on three different ships. He was promoted to lieutenant in 1935 and assigned to the aircraft carrier USS Saratoga in 1938.

During World War II Dufek commanded a flight training squadron, served as senior naval aviator in Algeria during the invasion of North Africa, assisted in the planning for the invasion of Sicily and Salerno and, after his promotion to captain and subsequent reassignment, the invasion of southern France. In September 1944 he assumed command of the escort carrierUSS Bogue, which sank the final German submarine lost in World War II.

Dufek retired from the Navy on 30 June 1955 and was promoted to the rank of rear admiral in recognition of his wartime accomplishments the same day. He continued to served on active duty so he could participate in Operation Deep Freeze.

In the spring of 1939 Dufek, at this time a lieutenant, requested and received an assignment with Rear Admiral Richard E. Byrd's third expedition to Antarctica, where he served as navigator of the USS Bear, the flagship of the expedition. In recognition of his many hours of exploratory flying over the South Polar continent Dufek later received the Antarctic Expedition Medal.

After a brief post-war stint in Japan, Dufek was assigned as chief staff officer to a U.S. Navy-Coast Guard task force to establish weather bases in the polar regions. While there he participated in Operation Highjump, a Naval expedition to Antarctica under the command of Admiral Byrd. He served as commander of the Eastern Group (Task Group 68.3) which consisted of a seaplane tender, a destroyer and a tanker.

During Operation Highjump he made the first flight over the Thurston Peninsula and later led the rescue six survivors of a crash of another flight (named George 1) over the same area.

He returned to Washington D.C. briefly, but by 1947 was back in the Antarctic, this time commanding a task force sent to supply existing weather stations and to establish new ones near the Pole.

In 1954 Dufek joined a special Antarctic planning group preparing for the Navy's Operation Deep Freeze, a scientific polar research expedition. When planning was complete Dufek was given command of Task Force 43 which, with more than 80 officers and 1000 enlisted men, three ice-breakers, and three cargo ships, was charged with logistics and support for the expedition. Dufek's first flagship for the operation was the attack cargo ship USS Arneb. He later transferred his flag to the icebreaker USS Glacier and was on board the Glacier when she completed a circumnavigation of the Antarctic continent later in the expedition.

Among other accomplishments, the task force established bases on Ross Island and in Little America, and on October 31, 1956,[3] Admiral Dufek and a crew of six[4] became the first Americans to set foot at the South Pole and to plant the American flag, and the first men to land on the pole from the air. On November 28, 1957, Dufek was present with a US congressional delegation during a change of command ceremony held at McMurdo Sound.[5] After Admiral Byrd's death, Dufek was appointed to succeed him as supervisor of U.S. programs in the South Polar Regions.